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Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, and BioData Catalyst. Learn more.

Terra uses pipelines (workflows) in Workflow Description Language (WDLs) for batch processing genomics data. Find here documentation on setting up and running WDLS using sample or your own data in a Google Cloud bucket.

  • Get started running workflows plus-icon minus-icon

    We think the best way to get started running workflows on Terra is to dive in and get started! The Terra QuickStart workspace is a hands-on practice that guides you through the process. You'll follow the steps below to get experience with increasi...
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  • Getting started with GATK workflows in the cloud FAQs plus-icon minus-icon

    If you're new to running GATK on a cloud-based platform, or new to Terra, this information will help get you started. From pre-processing raw sequencing data through variant calling and joint calling, showcase workspaces provide fully reproducible...
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  • Finding the workflow (method) you need (and its JSON) in the Methods Repository plus-icon minus-icon

    Many workflows already exist in Terra to help carry out different steps in your research journey. Below is a step-by-step outline for finding workflows in the Broad Methods Repository.  Note that FireCloud "methods" are called "workflows" in Terra...
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  • Importing a workflow and its configuration file from Dockstore into Terra plus-icon minus-icon

    Overview Dockstore is a GA4GH-compliant, open-source platform for sharing Docker-based tools, such as Terra-compatible workflows written in the Worflow Description Language (WDL).  This tutorial covers how to: Access and select a Dockstore workfl...
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  • What happens when you launch a workflow? plus-icon minus-icon

    What is going on behind-the-curtain when a you hit "Launch Analysis" from the Terra UI? This article helps you understand the components working in the backend - like what Cromwell does versus what Google Pipelines API does - to help understand wh...
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  • How to set up a workflow analysis plus-icon minus-icon

    This article explains how to set up (configure) your workflow analysis in the Terra UI. Note that this article is intended primarily for analyses using data from the workspace data table. Differences for using direct paths are noted in "hints" box...
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  • Getting workflows up and running faster with a JSON file plus-icon minus-icon

    Configuring with a JSON file helps avoid manually typing in workflow inputs and outputs and can get your WDL up and running in record time. This is especially useful when you want to quickly test that a WDL workflow can run successfully on Terra w...
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  • Monitor and troubleshoot in the Job History tab plus-icon minus-icon

    The Job History tab is your workspace operations dashboard, where you can check the status of past and current workflow submissions, drill down to see what’s going on and find direct links to all input and output files involved. This article walks...
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  • Scaling your workflow submissions plus-icon minus-icon

    The full power of working in the cloud is realized in your ability to scale. Many users today are already taking advantage of Terra and Google Cloud to submit workflows large in size and in number. Whether you are new to working in the cloud or yo...
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  • Create, edit, and share a new workflow plus-icon minus-icon

    Creating or editing a new Workflow in Terra currently requires working in the "Broad Methods Repository." This article includes step-by step instructions for how to 1. Create a new workflow2. Edit a workflow3. Share or clone a workflow as well as ...
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  • Creating a list file of reads for input to a workflow plus-icon minus-icon

    Raw genomics data is in the form of many reads from the sequencer. Since it would be messy and time consuming to type in the location of every one of these data files as input for a WDL, the input is often a 'list' file. This file is just a list o...
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  • Call caching: How it works and when to use it plus-icon minus-icon

    Call caching allows Terra's execution engine (aka Cromwell) to detect when a job has been run in the past so that it doesn't have to re-compute results. Learn how the call caching feature in Terra can save you time and money when you are repeating...
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  • How to use checkpointing to save on long-running tasks plus-icon minus-icon

    Running a long job but worried that you will lose your work if your job is interrupted in the middle of a task? Task-level checkpointing allows you to restart your workflow at an intermediate step, saving you from having to recompute work done up ...
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  • Saving storage costs by deleting intermediate files plus-icon minus-icon

    When running a workflow, intermediate steps often have outputs that are not very useful compared to the overall results. Complicated workflows can have a large number of large intermediates, which can increase the storage costs of a project. For e...
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  • Reference Disks in Terra plus-icon minus-icon

    Terra now includes the ability to automatically append a disk containing the HG 19/HG 38 references to your Google Virtual Machine, saving time otherwise spent on potentially slow localization of large reference inputs. If the checkbox labeled ‘Us...
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  • How does pipeline versioning work? plus-icon minus-icon

    Workflows in Terra Terra allows you to execute predefined bioinformatics workflows against data in your workspace. Each workflow is a chain of individual software tasks. Each task comprises a set of software instructions to execute (code), as well...
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  • Updating workflows to the latest version plus-icon minus-icon

    This article shows how to add a new version of a workflow to your Terra workspace in two instances - workflows hosted on Dockstore and those in the Broad Methods Repository.  Note for FireCloud users: you may be familiar with the "snapshots" crea...
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  • Default runtime attributes for workflow submissions plus-icon minus-icon

    Runtime attributes can be configured within a WDL's task block, but if no value is specified for any one of the customizable attributes your task will run with the default runtime attribute value. The chart below shows the defaults for each runtim...
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  • Google Cloud Resource Quotas: What are they and how do you request more? plus-icon minus-icon

      In the Google Cloud Platform (GCP), quotas specify how many resources, such as central processing units (CPUs) and persistent disks (PDs), can be used by a Google Project at any given time. Quotas prevent unforeseen spikes in usage so resources ...
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  • Why and how to use GPUs when running a workflow plus-icon minus-icon

    Graphical Processing Units (GPUs) are a kind of computer processor that can dramatically accelerate certain tasks that are specifically coded to use them, providing faster turnaround and cost savings compared to VMs that only use traditional CPUs....
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  • How to test workflows locally plus-icon minus-icon

    When creating WDL workflows, you can test on a local installation of the Cromwell execution engine prior to uploading and testing in Terra. Cromwell is the workflow execution service used to run and test WDL workflows. Cromwell is a Java applicati...
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  • Managing data and automating workflows with the FISS API plus-icon minus-icon

    FireCloud Service Selector (FISS) is a utility command module that allows API (Application Programming Interface) calls from the notebook to the workspace. Scripting with FISS is much like you would run on a local machine, but with Terra's built-i...
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  • Deeper dive - WDLs, workflows, and tasks plus-icon minus-icon

    Identifying workflow and task inputs and outputs Inputs and outputs are defined in the WDL.and can be at the "workflow" or the "task" level. Terra interprets the WDL and provides an input "form" to fill out. The outputs part of the form is optiona...
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  • Accessing archived workflow details plus-icon minus-icon

    To improve performance, Terra archives some workflow details (metadata) after a year. Read on to understand what workflow-level details are archived and how to retrieve them if you need them.  Contents - Archiving workflow details FAQs- How to acc...
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